Name: Christina Gaw

Date: 4/26/17

Rationale of Today’s Work: Today, we presented our presentations to classmates.

Tools used and/or Methods: GoogleSlides

1. Present GoogleSlides
   

   This is an overlay of our presentation for Friday.

Results:

• We received good feedback from Lathan and our peers about what to add to our presentation. We’re including more information about the background and a key to our graph.

Conclusions/next steps:

• The next step is to present at the CURES in BIO symposium.

Name: Christina Gaw

Date: 4/26/17

Question 1 Response:

Intralytix is a biotechnology company that focuses on discovering, producing, and marketing the use of bacteriophages to control pathogens in the environment, food industry, and medicine. However, when looking at their products, it seems like they have had more success or focused more on producing products related to food safety than any other category. Intralytix has more information on how phages work in comparison to traditional antibiotics. GangaGen is a biotechnology company that has specific interest in creating proteins products that prevent infectious diseases in areas that need the treatment. This includes drug resistant bacteria such as MRSA. They appear to be more involved in the medical aspect of science rather than industry and describe their goal of treating infections with the proteins they develop.

The best selling products for Intralytix are the products associated with food safety. They list three: ListShield, EcoShield, and SalmoFresh. The other products have have are in the process of development. It seems like they have had an emphasis on food safety. The best selling products for GangaGen is a recombinant protein P128. This protein binds to and kills Staphylococcus, a strain of MRSA.

The main struggles that these companies have to deal with are public marketing and credibility. Both websites share extensive information about how their products are applicable in the same situations as antibiotics. Intralytix has an FAQ page while GangaGen presents evidence from scientists studying the material. As well, both websites include the news of their product applications as well as publications and presentations. These all contribute to the credibility that the companies are attempting to establish. As stated in the book, some companies are wary of using new products and cautious to invest in unpopular methods. They have to target and invite the public to use their products. The companies do this by making management teams and contact information available and approachable. With these strategies, they hope to increase the popularity of the products.

Changes that have taken place since the writing include a wider selection of products for Intralytix. In the novel, Intralytix was focusing on food safety. Now, they have more products that demonstrate their research in the subject. It seems as though they are attempting to expand to phage applications in other live animals and that involvement is currently developing. GangaGen has recently had a news media appearance with their product. They presented data on preclincial trials by showing P128’s activity against MRSA and other Staphylococci. In the future, it appears that the company will focus on the medical applications of phages. Possibly, they might expand their research to include other types of bacteria that are affecting the regions they are targeting.

Name: Christina Gaw

Date: 4/24/17

Rationale of Today’s Work: Today, we worked on collecting data for the PowerPoint presentation on Friday.

Tools used and/or Methods: Internet, Google Docs

1. Input nucleotide sequence into MEME and research about interpretation of MEME data
2. Compare the output sequences of the promoter/motif analysis software and attempt to determine a consensus sequence

Results:

• We decided that we will be using the outputs from BPROM and MEME as well as the putative promoters found in DNA Master and comparing them to the consensus sequences presented at LeTourneau in order to create an overall consensus sequence for the Arthrophages.
  

  This is an example output of MEME for Nubia. The larger the letter, the more frequently it is seen. If two letters are present, both appear similarly. The whole genome was inputted into MEME.

Conclusions/next steps:

• The next step is to decided which posters the groups are presenting for URSA and practice presenting them.

Name: Christina Gaw

Date: 4/19/17

Rationale of Today’s Work: Today, we continued to work on our presentations.

Tools used and/or Methods: Internet, Google Docs

1. Read through article
2. Ran nucleotide sequences between reverse/forward gaps through SoftBerry and DNAMaster for comparison

Results:

• Lathan found an article for us to reference. In the article, their goal is similar to ours. They are finding promoters, but they are using a software program called MEME (Multiple Em for Motif Elicitation). Through MEME, they were able to determine a consensus sequence.
• We determined that we would try to match all of the outputs from the software and determine a consensus sequence from that.

We used MEME under motif discovery to find potential motifs for the sequences that we are interested in.

Conclusions/next steps:

• The next step is to work on collecting data and comparing the outputs from each of the software programs.

Name: Christina Gaw

Date: 4/12/17

Rationale of Today’s Work: Today, we continued to research for our project.

Tools used and/or Methods: Internet

1. We considered using SoftBerry and found a promoter finding software called BPROM.
2. We tried to input in sequences between reverse and forward genes to test out the program and learn more about how to interpret the results of BPROM.

Results:

• We will be using BPROM as a part of our research. It ranks the the promoters by the linear discriminant function and gives the -10 and -35 positions.
• BPROM appears to have some similarities with the consensus sequence that was presented LeTourneau.

This is an example output from SoftBerry.

Conclusions/next steps:

• The next step is to keep researching more about promoters and trying to find other software programs to do more analysis.

Name: Christina Gaw

Date: 4/10/17

Rationale of Today’s Work: Today, we decided on a topic to research for our independent project.

Tools used and/or Methods: Internet, Google Docs

1. Initially, we believed we were working to find the presence of endolysin and holin proteins in the phages by looking at the phage genomes. However, we decided to work with promoter sequences instead, building off of the research that was included in one of the posters that was presented at LeTourneau.

Results:

• We decided that we were going to work with finding promoter sequences in Arthrobacter and then trying to see if those sequences were also present in the three phage genomes that were annotated.

Conclusions/next steps:

• The next step is to begin researching the topic.

Name: Christina Gaw

Date: 4/5/17

Rationale of Today’s Work: Today, I researched topics for our independent project while the rest of my group, Caroline and Chrissy were working on their poster for the LeTourneau symposium.

Tools used and/or Methods: Internet, Notepad

1. I looked on Google Scholar for any ideas about what topics to do. A Google Doc was created, and I put the ideas into there.

Results:

• Some ideas that were included:

These were some of the ideas we were working with.

Conclusions/next steps:

• The next step is to select a topic to research and begin researching.

Name: Christina Gaw

Date: 4/3/17

Rationale of Today’s Work: Today, we worked on the abstract to submit for the symposium

Tools used and/or Methods: Microsoft Word

1. Work with Dr. Adair to finish editing the abstract we had written over the weekend.

Results:

• We finished the abstract and submitted it to the symposium.

Conclusions/next steps:

• The next step is to practice and look over the posters that we will be presenting at the symposium.

Name: Christina Gaw

Date: 3/29/17

Rationale of Today’s Work: Today, all groups took turns to present the one poster we were assigned to

Tools used and/or Methods: Microsoft PowerPoint

1. Present posters for URSA.

Results:

• Our group presented the poster in front of a professor as well as a few other students.

Conclusions/next steps:

• The next step is to work on the abstracts and posters for the LeTourneau Phage Symposium.

Name: Christina Gaw

Date: 3/27/17

Rationale of Today’s Work: Today, the class split up into two groups to practice presenting posters for URSA.

Tools used and/or Methods: Microsoft PowerPoint

1. Present posters for URSA within groups and in front of class

Results:

• The group we worked with for the URSA poster is the same group that we are presenting with during URSA except we will be presenting Stu’s poster.
• We learned how to explain the dot plot that was on Stu’s poster.

Conclusions/next steps:

• The next step is to present the poster at URSA Scholars Week.